4DXV

Crystal structure of Dihydrodipicolinate synthase from Acinetobacter baumannii complexed with Mg and Cl ions at 1.80 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RK8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22980.2M MgCl2, PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.35α = 90
b = 122.47β = 115.92
c = 52.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2011-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.861.2499.30.10314.45078750787
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.83980.562

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3RK81.861.245078750787272099.550.154540.154540.152170.19875RANDOM17.073
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.670.08-0.64-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.097
r_dihedral_angle_4_deg15.555
r_dihedral_angle_3_deg14.67
r_dihedral_angle_1_deg6.221
r_scangle_it6.054
r_scbond_it3.801
r_angle_refined_deg2.121
r_mcangle_it2.048
r_mcbond_it1.25
r_chiral_restr0.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.097
r_dihedral_angle_4_deg15.555
r_dihedral_angle_3_deg14.67
r_dihedral_angle_1_deg6.221
r_scangle_it6.054
r_scbond_it3.801
r_angle_refined_deg2.121
r_mcangle_it2.048
r_mcbond_it1.25
r_chiral_restr0.164
r_bond_refined_d0.027
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4390
Nucleic Acid Atoms
Solvent Atoms637
Heterogen Atoms9

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALAdata scaling